During the Alicorn Princess' recent Equestria's Royal Summit in Canterlot, to which Cadence does not show up, Queen Chrysalis makes an announcement: In three days she will unleash her "ultimate weapon" upon Equestria, and that Celestia, Luna, and Twilight must face it alone or else she will have it attack the civilians of a random city.
Earlier, after finding the Crystal Heart missing, Flash Sentry discovers a mysterious message from an anonymous voice claiming to know where the Crystal Heart has been taken, and joins Shining Armor and Princess Cadence on a quest to recover it.
Meanwhile, Spike has been kidnapped by Changelings, and Applejack, Rarity, Fluttershy, Pinkie Pie, and Rainbow Dash must go on a quest to rescue him.
Can these Equestria Heroes stop this twisted evil plot, and discover the truth behind it all?